A computational screen for type I polyketide synthases in metagenomics shotgun data.
BACKGROUND
Polyketides are a diverse group of biotechnologically important secondary metabolites that are produced by multi domain enzymes called polyketide synthases (PKS).


RESULTS
We have estimated frequencies of type I PKS (PKS I) - a PKS subgroup - in natural environments by using Hidden-Markov-Models of eight domains to screen predicted proteins from six metagenomic shotgun data sets. As the complex PKS I have similarities to other multi-domain enzymes (like those for the fatty acid biosynthesis) we increased the reliability and resolution of the dataset by maximum-likelihood trees. The combined information of these trees was then used to discriminate true PKS I domains from evolutionary related but functionally different ones. We were able to identify numerous novel PKS I proteins, the highest density of which was found in Minnesota farm soil with 136 proteins out of 183,536 predicted genes. We also applied the protocol to UniRef database to improve the annotation of proteins with so far unknown function and identified some new instances of horizontal gene transfer.


CONCLUSIONS
The screening approach proved powerful in identifying PKS I sequences in large sequence data sets and is applicable to many other protein families.
Foerstner
Konrad U
KU
European Molecular Biology Laboratory, Heidelberg, Germany.
Doerks
Tobias
T
Creevey
Christopher J
CJ
Doerks
Anja
A
Bork
Peer
P
D000818:Animals; D019470:Biolistics / Q000379:methods*; D019295:Computational Biology; D030541:Databases, Genetic; D003663:Decision Trees; D022761:Gene Transfer, Horizontal; D023281:Genomics / Q000379:methods; D006801:Humans; D016013:Likelihood Functions; D008390:Markov Chains; D055432:Metabolomics / Q000379:methods; D010802:Phylogeny; D048630:Polyketide Synthases / Q000032:analysis / Q000235:genetics*; D017422:Sequence Analysis, DNA
D048630:Polyketide Synthases